Justice League: Rise of a Spectre
by A-BOMBLIKEABOSS
Summary: After dying in his universe, Commander Shepard finds himself in another. But what he finds in this one is unexpected. Good thing he's not alone in this.
1. Chapter 1

**Hello, people, this is my first time writing a fanfiction, so feel free to comment to tell me if I missed anything or if I'm not doing something right. Now, with nothing else to say, I give you Justice Effect. **

**Chapter 1: A New World**

It was over. The Reapers were gone, but at the cost of Commander John Shepard's life. After uniting all the species in the galaxy, he made one last stand against the Reapers. But he knew that a full frontal assault against them would not work, so he went in with a small team. The two people that went with him were evacuated as the Reapers started attacking. But everyone else was killed by a Reaper laser. Shepard was the only one who survived. So he went in to the Conduit, which took him to the Citadel. His friend and mentor, Captain David Anderson was already in there trying to figure out how to destroy the Reapers. But the Illusive Man, leader of the pro human splinter group Cerberus took control of Shepard and made him shoot Anderson. After that, the Illusive Man killed himself leaving Shepard the only living person left on the Citadel. Near death, a being that called itself the Catalyst approached him and gave him three choices on what he could do to stop the Reapers. The first choice was to destroy them by shooting the core on his right, which would kill all synthetics including the Geth. The second choice was to control them, which would allow him to control the Reapers, but he would never see those he cares about again. The third and final choice was Synthesis, which would make everyone in the galaxy a new techno-organic species. Shepard made his choice as he walked toward the massive energy beam. As a walk became a full run, he sprinted to the energy beam and jumped into the beam. As he fell and started to disintegrate, he remembered those who died in the fight, his mentor, and the woman he loved, Miranda Lawson, then John Shepard was no more.

**Gotham City**

Batman was frustrated. After dealing with Catwoman, Bane, Scarecrow, Killer Croc, Two Face, Penguin, and Killer Moth, he was beginning to feel exhausted. "Let's put a smile on that face." Joker said as he pulled out his gun and fired a blank. "HAHAHAHAHA!" Joker laughed as he threw his recognizable sharp playing cards at Batman. "Give up, Joker." Batman said as he deflected the cards with his cape. Suddenly, a bright light flashed, making Joker and Batman to shield their eyes. When the light cleared, there stood a man in black and red armor with a helmet covering his entire face with a bunch of strange folded items on his back. "Where the hell am I?" Shepard said as he looked at his surroundings. He then noticed a man wearing a grey suit with a black cowl on his head as well as a black cape. On his suit was a bat symbol in the center. He then noticed a man in a purple business suit with pale white skin, green hair, and a sadistic grin on his face. "What do we have here?" Joker said as he looked at the new arrival with curiosity. Batman looked at Shepard with suspicion as he prepared a batarang behind his back, he then threw it at Joker as he ran up and punched him, knocking him out. He then payed his attention to Shepard as he said, "Who are you?" Shepard looks at him and says, "I could ask you the same thing." Batman looks at him as he responds. "I'm Batman, now who are you?" Shepard wondered on what to call himself when an idea came to him. "My name is Spectre, now can you tell me where the hell I am?" Batman looked at the Spectre in shock. _How does he not know where he is? _Batman thought as he looked at the Spectre. "You're in Gotham City." He said to Shepard as he prepared to take him down in case he's a threat. "Gotham City, sounds like a city on Earth." Shepard said as he looked at the dark knight in confusion. "The buildings look like Earth in the 21st century." Shepard said as Batman looked at him in realization. "You're from the future." He said as he prepared a smoke bomb. "Don't try to use that smoke bomb." Shepard said as Batman looked at him in surprise. "How did you-" "I'm detecting a smoke bomb near me, so I'm assuming it's coming from you." Batman threw the smoke bomb believing it would blind Shepard but he underestimated the first human Spectre as Shepard threw a biotic punch, knocking Batman off his feet. Shepard was about to knock out Batman when he heard an explosion from outside the building. He ran outside to see what was happening, and he saw a building was on fire. A group of people already made it out, but people were still trapped in the building. "Somebody do something." One of the people said as Shepard started to run towards the building. Batman got up and watched as the Spectre ran towards the burning building. When Shepard got inside, he saw that the fire was worse on the inside as he started to search for people who were stuck in the building. _I'm not letting anyone else die today _Shepard thought as he saw a group of people stuck in a room with the door on fire. He used his biotics to pull the door away from the entrance and went in to save the family. The people heard saw the door rip off the hinges as a dark blue glow surrounded it. What came in the room was a strange man wearing futuristic armor. "Are you okay?" he said in a distorted voice. They quickly nodded their heads as his body began to glow blue. "Come on, I can make a Barrier that will protect us." They quickly got up and ran to him as a dark blue barrier began to surround them. He started to walk out of the room, which they followed as the building started to collapse. "MOVE!" he shouted as he started to run out of the building with the others in tow.

He made sure everyone else made it out first before the barrier he made faded away. Shepard let out a sigh of relief as he prepared to leave the city, when suddenly a woman stopped him. "Vicki Vale, Gotham City News, who are you?" Shepard looked at the camera before saying, "My name is Spectre, that's all I'm going to say, ma'am." He started walking when his Omni-tool appeared on his arm, meaning something was up. He checked it and what he saw was impossible to believe. _The Normandy's here, but how?_ he thought as he called for a shuttle to pick him up. Thirty seconds later, a shuttle appeared making the reporters take pictures of it. He stepped inside and as the door closed he wondered who was piloting the shuttle. He took a look and who he saw made his eyes widen in shock. "Legion?"

**End of Chapter 1**


	2. Chapter 2

**Chapter 2: The Invasion Begins**

"Shepard-Commander." Legion said as Shepard looked at the Geth infiltrator that he knew as a friend. "How are you alive?" Shepard said as he wondered how Legion was talking to him. "I am unsure of how I am still alive." Shepard noticed that Legion had the Reaper upgrade in him, which made him self-aware. "I see you have the Reaper upgrades." Legion looked at him and his head tails flapped up. "Yes, I do." Shepard then asked the question he needed the answer to. "How is the Normandy here?" Legion looked at Shepard as he replied, "I woke up on the Normandy, but EDI says I was in an alternate reality." Shepard's eyes were as wide as dinner plates at that statement. "An alternate reality?" he asked. "Yes, we will have to talk to EDI about this." Legion said as they docked in the Normandy. As they got out of the shuttle, they heard an all too familiar voice, "Shepard, Legion, you're alive?" Shepard's eyes widened again as he turned around to see none other than the tank-bred Krogan, Urdnot Grunt. "Grunt, you're alive too?" He asked as he wondered how two dead crewmembers were talking to him. "What is going on is this some weird dream?" "This is not a dream, Shepard," a familiar low voice said Shepard, Grunt, and Legion turned to see the former Drell assassin, Thane Krios. "This is indeed real." Shepard was completely shocked to see not one, but three of his former crew alive and talking to him. "Thane?" he asked. Thane nodded as he looked around the Normandy. "It appears that we are the only ones on the Normandy." Then a familiar female voice said, "Not just you four." Shepard and the others turned to see the Asari Justicar Samara with them. "Samara, you're alive." Shepard said as he walked over to Samara and shook her hand. "But one question, how are we all still alive?" Shepard asked as he looked at everyone who was in the room with him. "I believe we have been given a second chance, or a third in your case." Samara said as the last part was directed at Shepard, as this had died before, but was brought back by Cerberus. "Ha-ha, very funny." Shepard said as he looked at everyone around him. "Well as far as I can tell, this reality is 21st Century Earth, and there appears to be costumed vigilantes and criminals." he said as he thought of an idea. "Well we need to find a way to blend in the community." Shepard said as he saw everyone nods at this suggestion. "It would be a way to find out where we are." Samara said. "Shepard, I suggest that we all prepare for tomorrow." A familiar mechanical female voice said as Shepard smiled. "EDI, somehow I knew I would find you on the Normandy." he said as they all nodded their heads. "I agree with EDI, we should prepare for tomorrow." Thane said as they all left for their quarters. Shepard smiled; at least he wasn't alone in this new reality.

**The next day…**

Shepard was sleeping peacefully when suddenly the alarms went off, he shot up, and eyes wide open as he asked, "EDI, what's going on?" "It appears that Earth is under attack by an unknown force," she said as he slipped into his N7 armor. "Tell the others to meet me at the shuttle bay." "Of course." she replied as he ran towards the shuttle bay door. When he got there, there was Legion, Grunt, Samara, and Thane waiting for him. "Get in the shuttle." he said as they all got in the shuttle and Legion got in the pilots seat. The shuttle then left the Normandy as it headed towards Earth. "EDI, what's the situation right now?" "It appears that all the world's nuclear missiles have been disabled, but there appears to be a group of people with powers fighting some of the aliens." EDI replied as he decided what to do. "Take us to them." Shepard said as Legion flew the shuttle towards the heroes.

**Meanwhile…**

Superman and the others were having a hard time dealing with the alien attackers as they kept attacking. He, J'onn, Flash, Batman, Hawkgirl, Lantern, and the new arrival were about to be overwhelmed when suddenly a advanced aircraft appeared behind them and the doors opened to reveal a blue skinned woman who looked human but had strange tentacles on her head and a green skinned humanoid that looked like a lizard. Both were carrying rifles. "GET DOWN!" the blue skinned woman shouted as they opened fire on the aliens, which ripped them to shreds. The heroes ducked as they started to fire. The remaining aliens changed their arms to blades as they charged only for them to suddenly burst into flames. The heroes turned around to see a huge creature holding a shotgun with a red clip sticking out at the aliens so they figured he was the one who set them on fire. When the remaining aliens were destroyed, the heroes rose up to greet the new arrivals. The three that they saw jumped out of the shuttle, but then a man wearing red and black armor with an N7 symbol on his chest plate hopped out. Batman immediately recognized him. They then saw a strange robot walk out of the shuttle that appeared to have one eye and three fingers. All of them had weapons on their backs. They started to walk towards the heroes when Lantern held up his hand with his ring pointed at them. "Hold it, identify yourselves!" They stopped and looked at him as Shepard replied, "Keep your shirt on, we're not going to attack you." Lantern gave him a look that said he didn't believe him. "Uh huh, and what makes you think I'll do that?" Shepard sighed, "If we were with them, why would we attack them or we would've simply started shooting you." That last statement made the heroes tense as Batman said, "Then why are you here?" Samara then said, "We wish to help." Superman then said, "Lantern, we need all the help we can get." Lantern looked at Superman for a minute before lowering his ring. "Alright, but can you at least tell us who you all are." Batman immediately said, "I know one of them, the one in black and red, he called himself Spectre." Shepard looked at Batman and replied, "Hello again, Batman, as for the rest of you, who are you?" "I'm Superman, this is J'onn J'onnz, Green Lantern, Flash, Hawkgirl, and I'm not sure who she is." the man of steel said indicating the other woman. "I am Diana, princess of Themiscyra, I came here because I could not stand idly by while the world suffers." the woman known as Diana said and Shepard decided to introduce the others. He pointed at each of his team members. "This is Legion, that's Urdnot Grunt, Samara, and Thane Krios, now can someone tell me what the hell is going on here," he said as the heroes listened to J'onn tell his story. Now, they had to come up with a plan to defeat the aliens. "We need to destroy those factories!" Diana shouted as they saw a black cloud forming from the factories. "I agree with Diana, those factories are our top priority." Diana looked at Shepard with a smile on her face. She did not expect a man to agree with her. Lantern then said, "This is no time for amateurs or people with fancy weapons." Grunt then did something that made Shepard and the others look at him in amusement. He head-butted Lantern knocking him to the ground. "My krant are not amateurs." Grunt said as Lantern was holding his head after what Grunt did. He then said, "What kind of species are you, I've never seen anyone like you during my time as a Lantern." Thane then said, "Not now, but you will get your answers soon." "We will need to split into teams." Legion said as Flash zoomed to Diana, "Dibs on the Amazon," he said. Shepard walks over to J'onn. "Thane and I will go with J'onn, we need to know exactly what we're dealing with, Grunt, Legion, Samara, you guys clear out the aliens around the world." Thane walked over to Shepard as the others got back in the shuttle and took off."I shall go with J'onn as well." Diana said as she walked away from Flash and over to Shepard, Thane and J'onn. "I'll go too, like Spectre says, we need to know what we're dealing with." Batman says as he walks over to Shepard and the others. "Then it's settled, now we take back Earth," Shepard said as they all left to take out the factories on Earth.

**End of Chapter 2**


	3. Chapter 3

**Chapter 3: Fall of a Spectre**

Shepard, Batman, Diana, Thane, and J'onn were at the factory in Egypt that was recently made so that meant it wasn't fully guarded yet. "Hiding is not the Amazon way!" Diana said as she was not wanting to wait and hide. "We need to find a weak point, we will attack when we find it." Thane said as Diana slowly agreed with him. "Until then, we wait for J'onn to return." Said Martian came phasing through the ground. "Their defenses are low, we need to find an opening." Diana flew off towards a walker immediately after J'onn was finished talking. Shepard and Thane were going to help her when Batman held up his hand. "Wait, lets see what she can do." he said as she pulled a golden lasso around the walker and tipped it over making a hole in the factory. "There's your opening," she said as if she was better than them. They started to advance into the factory when Shepard, Thane, and Batman noticed the aliens running away from the spot where sunlight was coming from. "Are you thinking what I'm thinking?" Shepard said to Thane and Batman. "They must have a weakness to the sun." Thane said as Batman nodded his head. They ran to catch up with J'onn and Diana as they noticed the paths keep getting blocked. "It's like they know where we are." Batman said as he looked at J'onn whose eyes were glowing. "Superman and Hawkgirl have failed," he said as Shepard said, "Are you sure?" "They have been taken to be prisoners or used for… feeding." The others were shocked, but now they knew they had to destroy this factory. Shepard decided to check on the others. "Grunt, are you okay?" he asked as he contacted the tank-bred Krogan "You've called at a really bad time, Spectre, we're being surrounded!" he said as the sounds of gunfire could be heard. "I AM KROGAN!" Grunt screamed into the comm as they heard him fire his shotgun. "Get out of there, Grunt, head back to the Normandy," he said as he cut the comm. "How are your friends doing?" Batman asked him. "They're being surrounded, so I told them to retreat for now," he said as J'onn told them that they had to get the core out of the factory. Diana, Thane and Shepard distracted the aliens while J'onn and Batman got the core. "Let's go!" Shepard yelled as he and Thane opened fire on the aliens that tried to attack Batman. As they were leaving, the path started to close. Shepard then used his Biotics and pushed Diana and J'onn towards the other side of the path as it closed. "NO! BATMAN! THANE! SPECTRE!" Diana screamed as she pounded the wall only to see lasers hitting the wall. "No," she said as J'onn said, "They are gone." He said hoping his shielding would work. She nodded her head sadly as they walked out of the factory, now more determined to defeat the aliens.

**On the other side…**

Shepard, Thane, and Batman were staring down the aliens pointing their weapons at them. Batman closed his eyes as they fired, but nothing happened. He opened his eyes to see Thane's arms glowing dark blue as he had thrown up a Barrier surrounding them as the aliens lasers bounced off the barrier. "We need to get out of here," he said as he started to walk towards the exit with Batman and Shepard in tow. Shepard started shooting the aliens to distract them from Thane. As they were nearing the exit, Shepard pulled out some cluster grenades. "Eat this!" he shouted as he threw them at the aliens and exploded on contact. They reached the outside of the factory as Shepard's Omni-Tool appeared shocking Batman. "What is that?" Shepard looks at him before saying, "I'll explain later." Thane then let the Barrier fade away before falling to the ground. "What's wrong with him?" Batman asked as he and Shepard helped him up. "Thane never made a Barrier that size before, so he's not going to be using his Biotics for awhile." Batman did not know what Biotics were, but he decided not to ask yet as Shepard Omni-Tool appeared again. "What are you doing?" he asked Shepard as a shuttle appeared in the sky. "Taking us to the Normandy," he said as they got in the shuttle. When they got in they heard a voice familiar to Thane and Shepard, though not familiar to Batman. "Spectre, you're alive?" Thane and Shepard as the pilot turned out to be none other than Kasumi Goto. "Kasumi?" Shepard asked wondering how Kasumi got here. "Yep, I'm your pilot," she said cheerfully as they left the Earth's atmosphere to the SSV Normandy. Batman's eyes widened as he saw the ship. _He has a ship too? _he thought as they docked onboard the Alliance vessel. "Where did you get this?" he asked Shepard as he and the others got off the shuttle to see Grunt, Samara, and Legion waiting for them. "I'll explain later, but right now, we need to come up with a plan to take out their main factory." He said as they all agreed with him. _First the Reapers, now these guys, my day just keeps getting better _he thought as he started explaining his plan to everyone.

**End of Chapter 3**


	4. Chapter 4

**Chapter 4: The Last Stand**

**On the Normandy…**

Batman was in the Normandy's lab trying to reverse the ion flow of the core that Thane, Shepard, and he took from the factory. He was surprised that this ship had a lab, but he wasn't complaining since they were in the middle of an invasion. He had asked Shepard where he got the supplies. He said, "I'll explain later." Batman didn't like his question being left unanswered, but he knew that Shepard would tell him and the others soon enough. He finally finished what he was doing when the door opened and Thane came in. "Meet us in the briefing room when you are done." he said as Batman picked up the core and followed Thane. When they got to the room, Kasumi, Samara, Grunt, Legion, and Shepard were waiting for them. "Did you finish reversing it, Batman?" he asked as Batman nodded his head. "Yes, but are you sure your plan is going to work?" he asked as Shepard said, "My plans never failed before, I just hope the others don't get caught in the crossfire," he said as they all got in the shuttle and headed for the main factory.

**Metropolis…**

The shuttle landed on a rooftop and Shepard and the others stepped out. "Alright, once we're inside, we'll have to make sure they don't find us," he said as they all nodded their heads as he handed Batman a comm. "Take this, you'll be able to communicate with as long as you stay on this frequency," he said as he gave Batman the frequency to communicate with them. "Alright, let's go." Shepard said as they started to approach the factory. When they got inside, they made sure that they were not seen and when they got to the center of the factory, they saw what appeared to be a giant heart torturing a green alien that they all asummed was J'onn and Superman and the others being restrained. "Let him go!" they heard Superman yell as he tried to free himself, as did the others. "You are hiding something, what is it?" the Imperium asked as he tortured J'onn in front of the other heroes. "What is it?" he asked again as the torturing got worse. "What is it?"

"NOW" J'onn said as he took on his human-like form as an explosion occurred. They all looked to see Batman standing near the reactor placing something in the hole he made then everything turned blue as the Senator Carr impostor said, "What have you done?" Batman simply replied, "Reversed the ion charge." The Imperium shouted, "Kill him!" "NOW!" a voice shouted that made the heroes except Batman widen their eyes as several aliens were obliterated by explosions as the heroes saw Shepard, Thane, and the others as well as a woman wearing a black outfit with a hood covering the top half of her face. "Guys," Flash said, as he was shocked to see them alive. "But how?" Diana said as she wondered how they escaped death. "I shielded them so they could not be detected." J'onn said as his strength returned. "Take them down guys," Shepard said as the others began to shoot down the aliens while Batman freed the others. As they were all free, they tore the ceiling to expose the sun, Superman's strength returned as the aliens started melting. The Imperium tried to escape, but was stopped by J'onn as he grabbed his tentacles. "You hide in the dark and shun yourselves from the sun, why? Does it burn your pale, putrid skin?" he said as the Imperium started to bulge. "Gross," Flash said as they started to evacuate the people who were captured.

"He's getting away." Lantern yelled as Hawkgirl tried to stop the Imperium from escaping Earth. "Not on my watch, EDI, bring in the Normandy." Shepard said as they landed on a rooftop and saw the Imperium's ship leave Earth. The heroes then heard a loud noise and turned to see the biggest ship they had ever seen. Everyone's eyes widened save for Shepard, Batman, Samara, Legion, Kasumi, Grunt, and Thane. Shepard and the others stepped onto the ship. "You guys coming?" Shepard asked as everyone got on the ship. They then felt the ship climb up the sky as it left Earth's atmosphere.

"Spectre, we are approaching the enemy ship," EDI said as everyone except Shepard and the others were wondering where the voice was coming from. "Hit them with everything we've got, EDI, everyone hold on," he said as the Normandy charged up the Thannix Cannons and opened fire on the Imperium's ship as it blew up on impact. "Alright, we should head back to Earth and take care of the remaining resistance." Shepard said as Lantern immediately said, "Not till we get some answers, who are you, where did you get this ship, what kind of-"

**(Paragon Action)**

"Lantern, I'll answer your questions when the time is right." Shepard said as he was turning the Normandy around. "Now, let's head back to Earth and take care of the remaining resistance." Shepard said as the Normandy headed back to Earth.

**Somewhere in the galaxy…**

A Thanagarian ship was scouting to see if there were any Gordanians in the area when suddenly a portal opens and a ship comes out a ship. The Thanagarians were unsure of what this was or where it came from, but they opened fire on the ship. Their weapons didn't leave a scratch on the vessel. The ship then fired their cannon, which completely decimated the Thanagarians. The ship then headed for Earth. The Collectors had returned.

**End of Chapter 4**


End file.
